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Bahamut Lagoon combines RPG mechanics with squad-based combat. Characters have HP, MP (SP for fighter characters), EXP, equipment, stats and class-specific, SP-draining special elemental abilities very much like traditional console RPGs. The player can explore his surroundings, talk to people and visit shops when not in battle, though to a limited degree as there is no world map and no way to leave the current area.

The game's core is its turn-based battles fought on a 2d grid. Characters are assembled into parties of four and the player allowed a maximum of six parties, which are usually well outnumbered. The two opposing sides act in alternating turns so that each party can move once and/or attack once a turn. Attacks are divided into distant and close-up combat. In the former, a party uses a special ability (e.g. casting fireballs, throwing lightning, healing allies) of one of its members at a distance. The range and possible area of effect damage vary per ability. If the attacking party has two or more characters with the same ability, they join in the action to multiply its effectiveness. Distant combat results in less money and generally less damage, but the target cannot retaliate. Distant attacks can also affect the field; fire and ice ignite or extinguish forests and melt or freeze ice, etc. Close-up, each unit in two adjacent opposing parties can act once. Very much like Final Fantasy SNES combat, they can attack an enemy, use an item or a special ability (though these can't be combined and most only affect one target instead of all) or defend.

Dragons have their own stats and gain experience like normal characters do. In battle, each party has a dragon attached to it and draws a large portion of its strength from that of its dragon: if a party's dragon is slain, the party will lose the ability to use special attacks and class-specific abilities for the remainder of the map. The beast acts as a very powerful autonomous unit that moves after its party does and it cannot be controlled beyond very simple commands, e.g. "Come!" Out of battle, dragons will eat anything and raising them by feeding them items is an important part of the game. Feeding can improve their stats as well as affect their behavior on the field, and the dragons develop into new forms as they grow.

The player can change the characters in each of the parties, their formation as well as what dragon represents them at will.

The story takes place in the sky world called Orelus. It begins at the prologue, a world being consumed by war and the skies turning to the purple color of sadness following the downfall of the Kingdom of Kahna. The Kingdom of Kahna gets conquered by the Granbelos Empire, headed by Emperor Sauzer, taking Princess Yoyo captive and forcing the defenders of the kingdom to withdraw in defeat. After the prologue, the horrible war has come to an end with the Granbelos Empire victorious over all the Lagoons of Orelus. Chapter 1 begins, with the rebel alliance called The Resistance, headed by Byuu, with backup from the former captain of the Kahna's Royal Guard, Matelite, and Sendak, magician and wise man from Kahna, being shaped up with the help of many other heroes from around the other kingdoms (Lagoons) also conquered by the empire, notably the great warriorTaicho from the kingdom of Mahal and his allies among others. As their first act they reclaim the former flagship from the Kahna Dragon Squad, called the Farnheit (Fahrenheit) and with this vessel, they set out on a journey to liberate the skies of Orelus, Lagoon by Lagoon from the clutches of the Granbelos Empire.

If the Resistance fails to win that war, the Granbelos Empire will oppress Orelus. In the fierce battles that follow, The Resistance manage to rescue Princess Yoyo from the Empire, thus claiming its first greater victory, yet, the time spent in captivity has made her heart change. Although she tries to hide it at first, her feelings for Byuu have now turned for the Imperial General Satha Palpaleos, who also seems to be in love with her in turn. Reflecting upon the fact that Kahna was conquered by the Empire as its guardian, The Holy Dragon, Bahamut (Apparently all major Lagoons across Orelus are home to an ancient holy dragon each), never woke up to defend it despite the previous king's attempts, they come then to the conclusion that in order to defeat Emperor Sauzer, they must gather the powers of the Holy Dragons to their side. Princess Yoyo seems to hold the power to communicate with the dragons and harness their powers. The legend of this is that the chosen one, the Dragnar, must control them and usher in a new era of prosperity. Should the person fail, calamities will wrack the world of Orelus. Emperor Sauzer at the same time has somehow acquired this power himself, and wishes to claim the power of the dragons for the empire. The Resistance continues to wage war across the skies of Orelus, liberating its Lagoons one at a time and gaining new allies of both their inhabitants and Holy Dragons, and soon the Empire begins losing its conquered dominions and begins to fracture as some of its most prominent generals, headed by Gudolf, begin plotting against their own emperor, whom they judge weak. Upon their contacting the Holy Dragons, both Yoyo and Emperor Sauzer begin falling ill, as it seems this act drains those linked to them of their spiritual energy. Yoyo, constantly accused by the Holy Dragons of being weak-minded endures, however, while Emperor Sauzer becomes gradually more ill. The awakening of the dragons cause the gates to another dimension, Altair, to open, and demonic creatures begin an invasion of the kingdoms of Orelus. On the eve of this, The Resistance finally arrives on Kahna and upon fighting an army of demons, they gain the alliance of General Palpaleos, secretly ordered to join by Emperor Sauzer himself, who has foreseen a great coming disaster which he feels only The Resistance can stop, even if that means waging war on the very empire he once served with zeal. Reunited with his love, Princess Yoyo, he assists in repelling an Imperial assault of massive proportions, thus, restoring Kahna her lost freedom on a battle in which many of the characters reflect upon their own emotions and motives.

The former resistance now becomes the Orelus Liberation Army and heads straight towards the hearth of the Empire, to end the war once and for all. After a great victory over the Imperial Flagship "Trafalgar", they find Emperor Sauzer, his illness advancing further, and take him in. Here he reveals with great courtesy that in order to obtain the ability to speak with the Holy Dragons he had done a pact with the demons from the other dimension. After admitting this, following a long period of agony, he finally dies, and his body is left to drift away in the never-ending skies of Orelus by Palpaleos, his closest friend. A different situation unfolds on the Granbelos Empire however, as the people witness the "official" burial ceremony of their beloved emperor and Gudolf climbs to the throne as the new ruler while a giant gate with the other dimensions opens itself over the skies of Granbelos. After a great battle, the Liberation Army defeats the Imperial Armies and penetrates deep into the imperial palace, where they defeat Gudolf, thus, claiming the final victory over the empire. Still, the greatest of all threats still looms over Orelus as the gates of Altair remain open. The brave Liberation Army, now with the help from all the Holy Dragons, including mighty Bahamut, fly the Farnheit inside the superior dimension, where they fight hordes of demons and their master, the most powerful of all dragons, Alexander. Alexander seeks to claim the powers of the other Holy Dragons in order to become unstoppable and rule over all worlds. The epic battle, on which the very survival of Orelus is to be decided, follows, and as Alexander is defeated, order is restored. Byuu and all of his friends make their farewells as they all return to their kingdoms to rebuild them under the newly restored order of peace, leaving Byuu along with Bahamut as the wandering guardians of the skies of Orelus.

Captain of the prestigious Kahna Dragon Squad, the young protagonist through which the player accesses the world of Orelus. A childhood friend of Princess Yoyo, he has a close affinity with and talent at handling dragons. Though demoted and thus outranked by Matelite, the resistance nevertheless seek his opinion and follow his leadership. The character is not shown to speak.

Palpaleos (パルパレオス Parupareosu)

Sauzer's long-time friend and right hand man, Palpaleos is a Cross Knight like Byuu. During the period in which the Empire had Yoyo captive, she and Palpaleos fell in love. Sauzer later orders Palpaleos to join the Liberation Army, as they are fighting to protect their world. In the end, he is hated by Granbelos citizens because of the war and he is killed by them.

Yoyo/Jojo (ヨヨ)

Princess and later Queen of Kahna and, therefore, able to understand and form a bond with the Holy Dragons. Kidnapped by the Granbelos Empire, she is rescued years later by the resistance forces, and with them, begins to seek out the Holy Dragons. Had been a dreamer, but begins to wisen up as the world changes and she grows older. She entertains the affections of a number of characters in the game. Becomes a Dragnar, after forming bonds with a number of the Holy Dragons.

Sendak (センダック Sendakku)

An old man with skills in magic, he acts as an advisor in the resistance forces. Promoted to the rank of Captain by Matelite, he leaves most decisions to Byuu, due to his indecisiveness. Able to summon the Holy Dragons along with Yoyo. Prone to rambling. Seems to have an attraction to Byuu.

Matelite (マテライト Materaito)

A middle-aged man serving as a guard to the royal family, Matelite is deeply enamored with Yoyo; as such, he creates a sort of rivalry between himself and Byuu. He oversees many of the strategies employed by the resistance, and unwillingly shares leadership with Byuu.

Rush (ラッシュ Rasshu)

A young, brash knight. He, along with Truce and Bikkebakke, was picked up as a street kid by Byuu and incorporated into the Kahna Dragon Squad. His strong will and opinions lead him to conflict with his superiors. Also in love with Yoyo.

Truce (トゥルース Turūsu)

A quieter, more thoughtful person than his friend, Rush. He thinks before he acts, and generally sees things with sense.

Bikkebakke (ビッケバッケ Bikkebakke)

Looks up to Byuu with great admiration. He begins to sell mushrooms to earn money, in hopes that after the war, he might be able to purchase a house in which he and his friends can reside.

Taicho (タイチョー Taichō)

A formal general of Mahal, which fell in its fight with the Granbelos Empire prior to the game's beginning. Being promoted by Matelite to second in command, he often takes Matelite's orders and broadcasts it to the rest of the resistance. Pained by the loss of his wife, Celine, at the hands of the Granbelos Empire.

Somewhat dense and very honorable, seems to have a crush on a certain wizard...

Mist (ミスト Misuto)

Vain, believing that every man on Fahrenheit is deeply in love with her. She sleeps constantly when not in battle, believing that it contributes to her beauty. Injured at the fall of Kahna, she is later found well, and joins the resistance.

Lukia (ルキア Rukia)

Calm and collected, she doesn't easily lose her composure on the battlefield. She seems to have a past with Donfan.

Jeanne (ジャンヌ Jannu)

Tomboyish. She is found hiding in Mahal, and joins with resistance from that point. She seems to have a past with Donfan.

Ectarina (エカテリーナ Ekaterīna)

A shy wizard who has a crush on the captain of Fahrenheit, Hornet.

Anastasia (アナスタシア Anasutashia)

Initially somewhat disdainful of the heavy armors, debating which class is better. Develops a crush on a certain heavy armor...

Melodia (メロディア Merodia)

The youngest member of the resistance; a wizard from Godland who likes to dance with the mini-devils.

Nelbo (ネルボ Nerubo)

A wizard from Campbell who joins when asked to by the Queen of Campbell. Close friends with Joy.

Frederica (フレデリカ Furederika)

Physically weak, she depends on medicine to avoid being bed-bound. Dreams of opening a pharmacy.

Diana (ディアナ Diana)

Loves to gossip. A friend of Ectarina who occasionally speaks for her.

Zora (ゾラ Zora)

Mother of Zora's Son; had served, at one point, the Queen of Campbell. She is an example of tough love, and can silence even Matelite.

Joy (ジョイ Joi)

A priest from Campbell who joins when asked to by the Queen of Campbell. Close friends with Nelbo.

Frenze (フルンゼ Furunze)

Had a friendship with Reeve until he became depressed. Spends his time in bed, thinking various things.

Reeve (レーヴェ Rēve)

Had a friendship with Frenze until the other became depressed, and is annoyed that Frenze is no longer as enthusiastic about being a lancer.

Zora's Son (ゾラのむすこ Zora no Musuko)

Actually named Orelus. He attempted to start a dragon squad of his own at Campbell, but failed miserably. He is also a great sweeper.

Donfan (ドンファン)

Believes himself to be debonair. Melodramatic, he hits on almost any woman he sees, failing spectacularly each time..

Sajin (サジン)

Found in Dafira and asks to join with the resistance; is silent and mysterious, as he joins the party, he can be hired to attempt the assassination of either Princess Yoyo, Matelite or a crew member (All as a matter of jokes), although he fails when paid to either kill Yoyo or Matelite on a very funny attempt, he is successful on killing the crew member.

Zeroshin (ゼロシン)

Found along with Sajin. Though they are always together he complains that they do not talk about anything but work and that he is not able to make new friends. Constantly writes letters to his mother.

Manyo (マニョ)

Speaks entirely through repetition of her own name ("Manyo! Manyo!"), with meanings translated in parentheses. Loves to dance.

Monyo (モニョ)

Speaks entirely through repetition of her own name ("Monyo! Monyo!"), with meanings translated in parentheses. Loves to dance.

Munyo (ムニョ)

Speaks entirely through repetition of her own name ("Munyo! Munyo!"), with meanings translated in parentheses. Loves to dance.

Wagahai (ワガハイ)

Unlike the other Mini-Devils, speaks normally. Is somber, which leads to some animosity between him and the other Mini-Devils. Joins in Godland.

Sauzer (サウザー Sauzā)

The Emperor of Granbelos, who succeeds in conquering the world of Orelus early in the game. However, his ambitions are greater than this, and he seeks to be the one to "open the door to the new era" spoken of in the Holy Dragons Legend. In order to accomplish this, he first captures Yoyo, and when she does not cooperate, he resorts to making a pact with several monsters in order to gain the power to communicate with the Holy Dragons. While this does give him the abilities he desired, it also causes him to become severely weakened and sick.

Satha Palpaleos (パルパレオス Parupareosu)

Sauzer's long-time friend and right hand man, Palpaleos is a Cross Knight like Byuu. During the period in which the Empire had Yoyo captive, she and Palpaleos fell in love. Sauzer later orders Palpaleos to join the Liberation Army, as they are fighting to protect their world. In the end, is hated by Granbelos citizens because of the war. In the end, he is killed by the Granbelos citizens.

Gudolf (グドルフ Gudorufu)

The most ambitious of the Granbelos generals, who plots to take control of the Empire himself. He does just this once Emperor Sauzer falls ill, and declares himself Emperor after Sauzer passes away. The Resistance Army fights him several times near the end of the game, and finally kills him in Granbelos Castle in Chapter 23.

Irvine (アーバイン Ābain)

A high ranking general who wields a powerful Excalibur Sword. He does not appear in battle until late in the game, and is the last Granbelos general (aside from Gudolf) to be killed.

Barbarella (バーバレラ Bābarera)

The only female general of the Granbelos Empire, who wields a whip in battle. She is the only general who does not have a single line of dialogue in the entire game. The Resistance Army does not encounter her until late in the game, where she participates in several battles before being defeated aboard the Empire's ship in Chapter 20.

Lestat (レスタット Resutato)

The Granbelos general who slew Taicho's wife during the Empire's invasion of Mahal. The Resistance Army battles him twice during the battles to liberate Mahal, and a final time when all the remaining Granbelos generals attack in Chapter 19. He possesses a distinctive laugh.

Radia (ラディア Radia)

Despite his youthful looks, this general is actually an undead sorcerer who leads a legion of other zombies. The Resistance Army battles him only once, in Chapter 13, where he is slain.

Persona (ペルソナ Perusona)

A Granbelos general who has the unusual hobby of "cleaning". The Resistance army battles him only once, in Chapter 12, where he is slain.

Zomberd (ゾンベルド Zonberudo)

A physically powerful general, whom the Resistance Army battles several times near the beginning of the game, and a final time in the big battle in Chapter 19.